ID code: '2RPT' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 9 C1' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' C A 3 alpha beta 73 93 79 76 109 C1' C A 4 alpha beta 104 124 110 107 140 C1' C A 5 alpha beta 135 155 141 138 171 C1' G A 6 alpha beta 166 189 172 169 205 C1' C A 7 alpha beta 200 220 206 203 236 C1' C A 8 alpha beta 231 251 237 234 267 C1' G A 9 alpha beta 262 285 268 265 301 C1' A A 10 alpha beta 296 318 302 299 334 C1' A A 11 alpha beta 329 351 335 332 367 C1' A A 12 alpha beta 362 384 368 365 400 C1' G A 13 alpha beta 395 418 401 398 434 C1' G A 14 alpha beta 429 452 435 432 468 C1' C A 15 alpha beta 463 483 469 466 499 C1' C A 16 alpha beta 494 514 500 497 530 C1' G A 17 alpha beta 525 548 531 528 564 C1' G A 18 alpha beta 559 582 565 562 598 C1' C A 19 alpha beta 593 613 599 596 629 C1' C A 20 alpha beta 624 645 630 627 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' C A 3 OK OK 78 74 91 77 107 C2' C A 4 OK OK 109 105 122 108 138 C2' C A 5 OK OK 140 136 153 139 169 C2' G A 6 OK OK 171 167 187 170 203 C2' C A 7 OK OK 205 201 218 204 234 C2' C A 8 OK OK 236 232 249 235 265 C2' G A 9 OK OK 267 263 283 266 299 C2' A A 10 OK OK 301 297 316 300 332 C2' A A 11 OK OK 334 330 349 333 365 C2' A A 12 OK OK 367 363 382 366 398 C2' G A 13 OK OK 400 396 416 399 432 C2' G A 14 OK OK 434 430 450 433 466 C2' C A 15 OK OK 468 464 481 467 497 C2' C A 16 OK OK 499 495 512 498 528 C2' G A 17 OK OK 530 526 546 529 562 C2' G A 18 OK OK 564 560 580 563 596 C2' C A 19 OK OK 598 594 611 597 627 C2' C A 20 OK OK 629 625 643 628 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' C A 3 OK OK 72 90 75 76 105 C3' C A 4 OK OK 103 121 106 107 136 C3' C A 5 OK OK 134 152 137 138 167 C3' G A 6 OK OK 165 186 168 169 201 C3' C A 7 OK OK 199 217 202 203 232 C3' C A 8 OK OK 230 248 233 234 263 C3' G A 9 OK OK 261 282 264 265 297 C3' A A 10 OK OK 295 315 298 299 330 C3' A A 11 OK OK 328 348 331 332 363 C3' A A 12 OK OK 361 381 364 365 396 C3' G A 13 OK OK 394 415 397 398 430 C3' G A 14 OK OK 428 449 431 432 464 C3' C A 15 OK OK 462 480 465 466 495 C3' C A 16 OK OK 493 511 496 497 526 C3' G A 17 OK OK 524 545 527 528 560 C3' G A 18 OK OK 558 579 561 562 594 C3' C A 19 OK OK 592 610 595 596 625 C3' C A 20 OK OK 623 641 626 627 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' C A 3 OK OK 74 89 71 73 103 C4' C A 4 OK OK 105 120 102 104 134 C4' C A 5 OK OK 136 151 133 135 165 C4' G A 6 OK OK 167 185 164 166 199 C4' C A 7 OK OK 201 216 198 200 230 C4' C A 8 OK OK 232 247 229 231 261 C4' G A 9 OK OK 263 281 260 262 295 C4' A A 10 OK OK 297 314 294 296 328 C4' A A 11 OK OK 330 347 327 329 361 C4' A A 12 OK OK 363 380 360 362 394 C4' G A 13 OK OK 396 414 393 395 428 C4' G A 14 OK OK 430 448 427 429 462 C4' C A 15 OK OK 464 479 461 463 493 C4' C A 16 OK OK 495 510 492 494 524 C4' G A 17 OK OK 526 544 523 525 558 C4' G A 18 OK OK 560 578 557 559 592 C4' C A 19 OK OK 594 609 591 593 623 C4' C A 20 OK OK 625 640 622 624 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' C A 3 OK OK 70 87 88 72 102 C5' C A 4 OK OK 101 118 119 103 133 C5' C A 5 OK OK 132 149 150 134 164 C5' G A 6 OK OK 163 183 184 165 198 C5' C A 7 OK OK 197 214 215 199 229 C5' C A 8 OK OK 228 245 246 230 260 C5' G A 9 OK OK 259 279 280 261 294 C5' A A 10 OK OK 293 312 313 295 327 C5' A A 11 OK OK 326 345 346 328 360 C5' A A 12 OK OK 359 378 379 361 393 C5' G A 13 OK OK 392 412 413 394 427 C5' G A 14 OK OK 426 446 447 428 461 C5' C A 15 OK OK 460 477 478 462 492 C5' C A 16 OK OK 491 508 509 493 523 C5' G A 17 OK OK 522 542 543 524 557 C5' G A 18 OK OK 556 576 577 558 591 C5' C A 19 OK OK 590 607 608 592 622 C5' C A 20 OK OK 621 638 639 623 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P C A 4 distorted distorted 75 99 100 101 129 P C A 5 distorted distorted 106 130 131 132 160 P G A 6 distorted distorted 137 161 162 163 194 P C A 7 distorted distorted 168 195 196 197 225 P C A 8 distorted distorted 202 226 227 228 256 P G A 9 distorted distorted 233 257 258 259 290 P A A 10 distorted distorted 264 291 292 293 323 P A A 11 distorted distorted 298 324 325 326 356 P A A 12 distorted distorted 331 357 358 359 389 P G A 13 distorted distorted 364 390 391 392 423 P G A 14 distorted distorted 397 424 425 426 457 P C A 15 distorted distorted 431 458 459 460 488 P C A 16 distorted distorted 465 489 490 491 519 P G A 17 distorted distorted 496 520 521 522 553 P G A 18 distorted distorted 527 554 555 556 587 P C A 19 distorted distorted 561 588 589 590 618 P C A 20 distorted distorted 595 619 620 621 ---------------------------------------------------------------------------------